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 External Resources

 1786https://www.addgene.org/1786  Addgene identifier (1786, reused)

 github.c...NA-seqhttps://github.com/vandijklab/HBEC_SARS-CoV-2_scRNA-seq  Dataset (Differentially expressed genes table, reused)

 figshare...235471https://figshare.com/articles/HCL_DGE_Data/7235471  Dataset (Human lung data, reused)

 gro-2/83594http://resolver.sub.uni-goettingen.de/purl?gro-2/83594  GRO.publications identifier

 GSE139522https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139522  NCBI GEO Dataset (GSE139522, reused)

 GSE145926https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145926  NCBI GEO Dataset (GSE145926, reused)

 NC_045512.2https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2  NCBI nucleotide (NC_045512.2)

 9606https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606  NCBI taxonomy (human, Homo sapiens)

 10090https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090  NCBI Taxonomy (mouse, Mus musculus)

 0000-0002-0642-1610https://orcid.org/0000-0002-0642-1610  ORCID identifier (Ludovico Cantuti-Castelvetri)

 0000-0001-7876-4607https://orcid.org/0000-0001-7876-4607  ORCID identifier (Ravi Kant Ojha)

 0000-0002-7759-6557https://orcid.org/0000-0002-7759-6557  ORCID identifier (Minou Djannatian)

 0000-0003-3556-647Xhttps://orcid.org/0000-0003-3556-647X  ORCID identifier (Liliana D. Pedro)

 0000-0002-2347-5397https://orcid.org/0000-0002-2347-5397  ORCID identifier (Suvi Kuivanen)

 0000-0001-7523-6622https://orcid.org/0000-0001-7523-6622  ORCID identifier (Jonas Franz)

 0000-0002-9433-9173https://orcid.org/0000-0002-9433-9173  ORCID identifier (Franziska van der Meer)

 0000-0001-5926-8608https://orcid.org/0000-0001-5926-8608  ORCID identifier (Tugberk Kaya)

 0000-0002-4555-6446https://orcid.org/0000-0002-4555-6446  ORCID identifier (Maria Anastasina)

 0000-0003-1528-044Xhttps://orcid.org/0000-0003-1528-044X  ORCID identifier (Leonora Szirovicza)

 0000-0003-4797-5481https://orcid.org/0000-0003-4797-5481  ORCID identifier (Allan Tobi)

 0000-0002-2229-6661https://orcid.org/0000-0002-2229-6661  ORCID identifier (Pamela Österlund)

 0000-0002-4533-0455https://orcid.org/0000-0002-4533-0455  ORCID identifier (Merja Joensuu)

 0000-0001-6400-1107https://orcid.org/0000-0001-6400-1107  ORCID identifier (Frederic A. Meunier)

 0000-0001-7060-5871https://orcid.org/0000-0001-7060-5871  ORCID identifier (Sarah Jane Butcher)

 0000-0001-6319-404Xhttps://orcid.org/0000-0001-6319-404X  ORCID identifier (Özgün Gökçe)

 0000-0002-9458-6385https://orcid.org/0000-0002-9458-6385  ORCID identifier (Tambet Teesalu)

 0000-0001-5699-214Xhttps://orcid.org/0000-0001-5699-214X  ORCID identifier (Jussi Hepojoki)

 0000-0003-2270-6824https://orcid.org/0000-0003-2270-6824  ORCID identifier (Olli Pekka Vapalahti)

 0000-0003-1766-5458https://orcid.org/0000-0003-1766-5458  ORCID identifier (Christine Stadelmann-Nessler)

 0000-0002-3585-559Xhttps://orcid.org/0000-0002-3585-559X  ORCID identifier (Giuseppe Balistreri)

 0000-0001-5329-192Xhttps://orcid.org/0000-0001-5329-192X  ORCID identifier (Mikael Jakob Simons)

 73https://prod.mbexc.uni-goettingen.de/literature/publications/73  Published Data Registry entry (MBExC)

 2/9https://rdp.sfb274.de/archive/2/9  Research Data Archive (supplemental material)

 043j0f473https://ror.org/043j0f473  ROR identifier (043j0f473, German Center for Neurodegenerative Diseases)

 05591te55https://ror.org/05591te55  ROR identifier (05591te55, Ludwig-Maximilians-Universität München)

 021ft0n22https://ror.org/021ft0n22  ROR identifier (021ft0n22, University Medical Center Göttingen)

 02kkvpp62https://ror.org/02kkvpp62  ROR identifier (02kkvpp62, Technical University of Munich)

 CVCL_0025https://scicrunch.org/resolver/CVCL_0025  SciCrunch identifier (RRID:CVCL_0025, Caco-2)

 CVCL_0045https://scicrunch.org/resolver/CVCL_0045  SciCrunch identifier (RRID:CVCL_0045, HEK293)

 SCR_007358https://scicrunch.org/resolver/SCR_007358  SciCrunch identifier (RRID:SCR_007358, CellProfiler)

 SCR_002285https://scicrunch.org/resolver/SCR_002285  SciCrunch identifier (RRID:SCR_002285, Fiji)

 SCR_002630https://scicrunch.org/resolver/SCR_002630  SciCrunch identifier (RRID:SCR_002630, GitHub)

 SCR_002798https://scicrunch.org/resolver/SCR_002798  SciCrunch identifier (RRID:SCR_002798, GraphPad Prism)

 SCR_003070https://scicrunch.org/resolver/SCR_003070  SciCrunch identifier (RRID:SCR_003070, ImageJ)

 SCR_014479https://scicrunch.org/resolver/SCR_014479  SciCrunch identifier (RRID:SCR_014479, Inkscape)

 SCR_014551https://scicrunch.org/resolver/SCR_014551  SciCrunch identifier (RRID:SCR_014551, Olympus cellSens Software)

 SCR_002629https://scicrunch.org/resolver/SCR_002629  SciCrunch identifier (RRID:SCR_002629, OMERO)

 SCR_002105https://scicrunch.org/resolver/SCR_002105  SciCrunch identifier (RRID:SCR_002105, Samtools)

 SCR_007322https://scicrunch.org/resolver/SCR_007322  SciCrunch identifier (RRID:SCR_007322, Seurat)

 SCR_011848https://scicrunch.org/resolver/SCR_011848  SciCrunch identifier (RRID:SCR_011848, Trimmomatic)

 science....sm.pdfhttps://www.science.org/doi/suppl/10.1126/science.abd2985/suppl_file/abd2985_cantuti-castelvetri_sm.pdf  Supplemental material

 science....st.pdfhttps://www.science.org/doi/suppl/10.1126/science.abd2985/suppl_file/abd2985_mdar_reproducibility_checklist.pdf  Supplemental material (reproducibility checklist)

 en.bio-p...bd2985https://en.bio-protocol.org/cjrap.aspx?eid=10.1126/science.abd2985  Supplemental material (protocol on request at bio-protocol.org)

 Q100750024https://www.wikidata.org/wiki/Q100750024  Wikidata ID